[gmx-users] about the traj modification

[zh.li]

Dear Justin,
     Thanks for your instant reply about my problem. I've already
finished the make_ndx part, choosing the "protein" option. But for
trjconv, how can I write the command line to have the prompt "Select
group for output"? Sorry, I'm really a beginner. Thank you!

Best,
Zhenwei

-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul
Sent: 2010年1月13日 0:21
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] about the traj modification



zh.li wrote:
> Dear all,
> 
>  
> 
>      I want to remove the water molecules in the original traj file 
> (run.xtc) to save the space, so that I should use the command
“trjconv”. 
> But I don’t know which sub-command I should use to realize that? Does

> anyone here know how to do it?　Thank you very much.
> 

You'll need an index group that defines all non-solvent atoms (easily
done with 
make_ndx).  Pass the index file to trjconv and simply choose your
non-solvent 
group when prompted "Select group for output."

-Justin

>  
> 
> Zhenwei Li
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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